SwarmDock and the Use of Normal Modes in Protein-Protein Docking

International Journal of Molecular Sciences

Iain H. Moal¹ 

[1] id="af1-ijms-11-03623">Biomolecular Modelling Laboratory, Cancer Research UK London Research Institute, Lincoln’s Inn Fields Laboratories, 44 Lincoln’s Inn Fields, London, WC2A 3LY,

关键词: elastic network model;    normal mode analysis;    particle swarm optimisation;    PSO;    protein flexibility;    RTB;    CAPRI;   

DOI  :  10.3390/ijms11103623

来源: mdpi

【 摘 要 】

Here is presented an investigation of the use of normal modes in protein-protein docking, both in theory and in practice. Upper limits of the ability of normal modes to capture the unbound to bound conformational change are calculated on a large test set, with particular focus on the binding interface, the subset of residues from which the binding energy is calculated. Further, the SwarmDock algorithm is presented, to demonstrate that the modelling of conformational change as a linear combination of normal modes is an effective method of modelling flexibility in protein-protein docking.

【 授权许可】

CC BY   
© 2010 by the authors; licensee Molecular Diversity Preservation International, Basel, Switzerland.